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12030 Commits

Author SHA1 Message Date
Oliver Henrich af0b5b0e84 Removed dead code 2017-03-22 16:23:29 +00:00
Oliver Henrich 7435084375 Verified oxDNA with modified nucleotide layout 2017-03-22 15:59:10 +00:00
Oliver Henrich 7a75cd111c Minor updates in documentation and setup tool, merge before upgrade to oxDNA2 2017-03-14 11:39:09 +00:00
Oliver Henrich 23b8287933 Updated documentation and simple setup tool 2017-03-14 11:36:44 +00:00
Steve Plimpton f871ecdc67 change to RCB cuts in load-balancing commands, also a new option for fix halt 2017-03-10 15:55:07 -07:00
sjplimp 470353e320 Merge pull request #408 from giacomofiorin/colvars-update-2017-03-10 
Colvars update 2017-03-10
 2017-03-10 14:51:16 -07:00
sjplimp ffe02d20ca Merge pull request #406 from stanmoore1/kokkos_bugfix 
Fix Kokkos issues
 2017-03-10 14:51:04 -07:00
Giacomo Fiorin f70752c18f Include PDF of Colvars doc missing in previous commit 2017-03-10 15:58:35 -05:00
sjplimp 07fcfd6d54 Merge pull request #405 from stanmoore1/ev_setup_kk 
Add alloc flag to ev_setup
 2017-03-10 11:01:51 -07:00
sjplimp c97feafca6 Merge pull request #407 from frobnitzem/master 
Add error check to lammps_gather_atoms/lammps_scatter_atoms in library.cpp
 2017-03-10 11:00:30 -07:00
sjplimp b20d95d495 Merge pull request #402 from timattox/USER-DPD_spelling 
Fix spelling "correction" from 3a054d1a: iterations not interactions and imd_writen not imd_written
 2017-03-10 10:59:43 -07:00
Giacomo Fiorin 0b4adaa9e6 Backport typo fixes that were not previously pushed to the Colvars repository 2017-03-10 09:24:46 -05:00
Giacomo Fiorin 5fe6206638 Update Colvars module to version 2017-03-10 2017-03-10 09:16:58 -05:00
David M. Rogers 65964f3b31 Add error check to lammps_gather_atoms/lammps_scatter_atoms in library.cpp 2017-03-09 16:49:07 -05:00
Stan Moore b28b84d444 Fix half from full nlist issue with Kokkos 2017-03-09 14:00:27 -07:00
Stan Moore a001a5ceb0 Fixing memory overflow issue in comm_kokkos 2017-03-09 12:20:49 -07:00
Axel Kohlmeyer 2ef713ea1b restore incorrect change due to spell checking in fix imd 2017-03-08 16:40:16 -05:00
Stan Moore 1f6c1942b3 Disable allocation of per-atom arrays in ev_setup for Kokkos styles 2017-03-08 12:42:44 -07:00
Stan Moore 683023d820 Adding alloc flag to ev_setup 2017-03-08 12:36:23 -07:00
Tim Mattox 42d3a8f498 Fix spelling "correction" from 3a054d1a: iterations not interactions. :-) 2017-03-07 15:41:06 -05:00
Steve Plimpton 79b005dc3d patch 7Mar17 2017-03-07 11:40:07 -07:00
sjplimp a2fa6ef452 Merge pull request #393 from akohlmey/small-bugfixes 
Small bugfixes
 2017-03-07 09:56:03 -07:00
sjplimp 920641bbff Merge pull request #399 from rbberger/docs_spelling_fixes 
Correct spelling errors in documentation
 2017-03-07 09:47:22 -07:00
sjplimp c2aabdec22 Merge pull request #398 from stanmoore1/kokkos_changes 
Kokkos changes
 2017-03-07 09:46:54 -07:00
sjplimp e4aa735a68 Merge pull request #395 from timattox/USER-DPD_bugfix 
USER-DPD: a variety of small but important bugfixes
 2017-03-07 09:46:40 -07:00
sjplimp 4af6557568 Merge pull request #394 from jaapkroe/kolmogorov-crespi 
Added Kolmogorov-Crespi potential
 2017-03-07 09:46:08 -07:00
sjplimp 0798885bdb Merge pull request #389 from akohlmey/update-agni-potential 
update AGNI potential for Al, reference runs and output and citation
 2017-03-07 09:35:31 -07:00
sjplimp 020e75e7ef Merge pull request #386 from akohlmey/doc-consistentcy 
improve consistency of manual
 2017-03-07 09:33:14 -07:00
sjplimp d6866f1cfd Merge pull request #376 from v0i0/airebo-bondorderLJ-fixes 
Fixes for PairAIREBO::bondorderLJ
 2017-03-07 09:32:30 -07:00
Steve Plimpton efaa4c6710 new neigh_modify exclude option, other SNAP changes 2017-03-07 09:31:12 -07:00
Richard Berger 08baaa9d8e Fix more typos in tools 2017-03-07 01:00:25 -05:00
Richard Berger 359af419a7 Fix typo in python README 2017-03-07 00:58:35 -05:00
Richard Berger 21be86c423 Fix typos in txt2html 2017-03-07 00:58:03 -05:00
Richard Berger d6800405a5 Fix more typos in examples 2017-03-07 00:57:23 -05:00
Richard Berger 3a054d1a82 Fix more typos in src files 2017-03-07 00:55:01 -05:00
Richard Berger 007f3c66a0 Third batch of spelling fixes in manual 2017-03-07 00:51:31 -05:00
Richard Berger 32708860a9 Add remaining false positives 2017-03-07 00:27:35 -05:00
Richard Berger fc9eebb936 Added spellcheck utility to documentation build 
Uses the sphinxcontrib-spelling extension and requires PyEnchant and
aspell-en to be installed.

Adds the optional make target 'spelling' which produces the file
spelling/output.txt. It contains all words it detects.

Due to the large number of false positives, words in
utils/sphinx-config/false_positives.txt are ignored.
 2017-03-05 21:23:41 -05:00
Richard Berger dd76ac5010 Fix typos in tools folder 2017-03-05 21:18:01 -05:00
Richard Berger 17486a9319 Convert USER/lb/polymer files to UNIX line endings and remove trailing whitespace 2017-03-05 21:16:21 -05:00
Richard Berger 778a79b8ee Fix typos in examples folder 2017-03-05 21:10:33 -05:00
Richard Berger 7dd60f9737 Fix typos in src files 2017-03-05 21:03:40 -05:00
Richard Berger 084d831bce Second batch of spelling fixes in manual 2017-03-05 21:02:51 -05:00
Richard Berger e261bef7bb Spelling fixes in source files 2017-03-05 18:30:39 -05:00
Richard Berger fd78486086 First batch of spelling fixes in manual 2017-03-05 18:27:38 -05:00
Stan Moore 6382d3c89a Improving memory access in comm_kokkos 2017-03-03 09:14:47 -07:00
Tim Mattox 763a00e8b0 USER-DPD: pair_multi_lucy_rx bugfix for systems with multiple atom types 2017-03-03 09:29:17 -05:00
Axel Kohlmeyer ce1a3f25e1 Merge branch 'pair_write_fix' of https://github.com/andeplane/lammps into small-bugfixes 2017-03-03 08:11:55 -05:00
Anders Hafreager eaf7ed7707 Print error if pair_write does not get correct number of arguments 2017-03-02 21:25:27 -08:00
Tim Mattox 9a560b9091 USER-DPD bugfix: make atom_vec_dpd work properly with atom_vec_hybrid. 
We were sending too much data during pack_comm_hybrid/unpack_comm_hybrid.
 2017-03-01 15:22:28 -05:00